Publication of first draft of the tree of life
We are excited to publish the first draft of the Open Tree of Life in PNAS:
Scientists have used gene sequences and morphological data to construct tens of thousands of evolutionary trees that describe the evolutionary history of animals, plants, and microbes. This study is the first, to our knowledge, to apply an efficient and automated process for assembling published trees into a complete tree of life. This tree and the underlying data are available to browse and download from the Internet, facilitating subsequent analyses that require evolutionary trees. The tree can be easily updated with newly published data. Our analysis of coverage not only reveals gaps in sampling and naming biodiversity but also further demonstrates that most published phylogenies are not available in digital formats that can be summarized into a tree of life.
This is only a first draft, and there are plenty of places where the tree does not represent what we know about phylogenetic relationships. We can improve this tree through incorporation of new taxonomic and phylogenetic data. Our data store of trees (which contains many more trees than are included in the draft tree of life) is also a resource for other analyses. If you want to contribute a published tree for synthesis (or for analyses of coverage, conflict, etc), you can upload it through our curation interface.
Other pages and links:
- supplemental doc with details about methods
- Dryad data package when you can download the taxonomy and the tree
- infographics about the tree of life
- interactive tree browser
- roundup of news coverage
Many thanks to all of the people that provided data, discussion, review, curation, and code and of course to NSF Biology for funding this work!
Where are all the fossil taxa in this tree? Searching for them usually gets me either an error message about them being flagged “incertae sedis” or no results.
There was nothing at all in Archosauria except extant crocodilians and a small number of extinct near-relatives, plus Neornithes. The 500 or so species of non-avian dinosaurs were missing entirely from the tree. No pterosaurs, ornithischians, or sauropods were in the taxonomy at all, and only a small number of non-avian theropods were.
Mammals fared a bit better, but the lack of stem-synapsids in the tree synthesis database leads me to question the validity of the entire tree. Dimetrodon was missing from the taxonomy entirely, as was Juramaia, the latter of which as the earliest known eutherian is unacceptable. Important stem-mammals like Eomaia and Morganucodon should have been used to generate the tree as well, but they were also left out of the tree synthesis database.
Furthermore, important transitional fossils like Pikaia (missing from the taxonomy entirely!), Tiktaalik, Australopithecus, Ambulocetus, Archaeopteryx, and Hyracotherium were left out of the tree synthesis database. The lack of these and other intermediates indicate that far from being a comprehensive tree of life, this is a series of leaves with no branches, trunk, or roots. This tree should not have been allowed to be released in its current state.
September 23, 2015 at 3:32 am
I apologize for my tone in the previous post. I recently reviewed the conversation on Reddit and learned there are plans to introduce more fossil taxa in the future. I understand this is sort of a rough draft and not quite a finished product yet.
I would still have preferred to see some of the more important stem-members of different lineages included from the start, though.
September 23, 2015 at 7:25 am